An aching back and a sore shoulder don’t often agree with 54 holes of golf.

Such ailments plagued the pairing of Fred Couples and John Daly, but did little to slow the duo as they cruised to a 12-under-par 60 on Sunday in the final day of the Merrill Lynch Shootout at Tiburón Golf Club in North Naples.

Daly and Couples turned in a three-round total of 194 and placed ninth in the field of 12 teams. They finished seven strokes behind the winning pair of Woody Austin and Mark Calcavecchia. But with a separated shoulder bothering Daly and chronic back pain flaring up for Couples, some joked that the two might not make it to the finish.

“I tell you what, it’s frustrating. Really is frustrating,” said Daly, 41.

“This is the first really broken — besides my fingers, this has really been the first thing that’s been broken outside this hand.”

Daly injured a rib after trying to stop himself in mid-swing when a fan took a picture at the Honda Classic in March. He’s since complained of his shoulder popping out “seven or eight times,” which has forced him to curtail his signature, hammering drives. Daly has worked with a team physician from his alma mater, the University of Arkansas, and, on his advice, he took the last few weeks off to rest the shoulder.

The injury has also forced him to withdraw from a number of tournaments, pushing him to 188th on the money list. Daly finished 33rd on that same list in 2005.

Couples, 48, has suffered from back pain for more than a decade, but the problem resurfaced in April during his play at the Masters Tournament. Since then, Couples has competed in just one other professional round, the LG Skins Game in late November.

“To sit around for eight months and not play any golf, I thought, you know, would help,” said Couples. “But it is what it is. There’s not a whole lot I can do about it.”

Their collective time off led to rusty play Friday when the duo turned in the highest score of the field with a 70. After two days of pro-am events and 36 holes of professional play, they seemed to have found their footing Sunday, chalking up seven birdies on the front nine to tally a 29 at the turn. They put away five more birdies on the back.

“I mean, I feel for Freddy,’’ Daly said. “This is kind of the first time it’s ever happened to me. I’ve been very lucky. I’m a very flexible guy. But what he’s going through the last 10 years of his career, one of the greatest players that ever played and stuff like this that you have no control over, it really frustrates you.

“I mean, this year has just sucked for this. It really has. It’s unfortunate it happened, and it shouldn’t have happened, but I understand how he feels now.”

Only time will tell what the future holds for each player.

Speculation abounds on Couples’ possible retirement, something he admitted to pondering.

“I’m not the kind of guy that wants to half do it,” said Couples.

“I enjoy playing at home … to go out and play, to pass time. But that’s something that I don’t want to not be able to do.

“That would bother me more than, at this time, not playing the tour.”

After five consecutive days of golf, Daly said his shoulder felt good. He will start training with famed golf instructor Butch Harmon later this month, an opportunity he is very much looking forward to.

“I’m going to work with Butch after Christmas, probably during the week of the Mercedes(-Benz Championship), which I’m not in. He’s going to help me get ready for (the Sony Open),” said Daly.

“Butch will push you. I never had anybody push me to do things. I think Freddy works with Butch and he’s helped a lot of the guys.”